AlphaFold reveals ‘family tree’ of viruses including hepatitis C, dengue and Zika

Hello Nature readers,
Today we learn that mosquito-borne diseases are on the rise in Europe, trace the evolution of flaviviruses with the help of AlphaFold and discover the efforts to build ‘foundational’ AI models trained on vast biological datasets.

AlphaFold reveals how viruses evolved

Protein structures predicted by AI models have revealed some twists in the evolution of flaviviruses — a group that includes hepatitis C, dengue and Zika viruses. Researchers used DeepMind’s AlphaFold2 and Meta’s ESMFold to generate more than 33,000 predicted structures for proteins from 458 flavivirus species. They already uncovered some surprises. For example, the hepatitis C virus infects cells using an entry system similar to one seen in the pestiviruses — a group that includes animal pathogens like swine fever. Another big surprise was the discovery that some flaviviruses have an enzyme that seems to have been stolen from bacteria.

Mosquito-borne disease cases rising

Rising temperatures and heavy rainfall are turning Europe into a breeding ground for mosquito-borne diseases, researchers warn. New figures show there have been 715 locally acquired cases of West Nile virus across 15 European countries this year. Climate change is creating cosy conditions for Culex pipiens and Aedes albopictus mosquitoes in places they couldn’t previously thrive, extending their range and the transmission period of the diseases they carry. “We are faced with a problem where new places could become hotspots of transmission that were not prepared for this before,” says genetic epidemiologist Houriiyah Tegally.

A portrait of pregnancy brain changes

Researchers took 26 MRI scans of one woman’s brain during her first pregnancy to chart how her brain changed in unprecedented detail. The 38-year-old woman, who conceived using IVF, gave scans and blood samples starting before conception and extending for two years after the birth of her child. The data show a widespread decrease in grey matter, and a temporary increase of white matter toward the end of the second trimester, both linked to hormonal changes. “The maternal brain undergoes this choreographed change across gestation and we’re finally able to observe the process in real time,” said neuroscientist and study co-author Emily Jacobs.

‘Zeta-class’ supercomputer six years out

Work to develop a supercomputer that could out-pace the world’s current fastest by 1,000 times is officially underway. Expected to cost the Japanese government around US$775 million, the Fugaku Next machine should be online by 2030. The world’s fastest current supercomputer functions in the realm of one quintillion (1017) calculations per second, or exaFLOPS. Fugaku Next is expected to operate in the realm of zetaFLOPS, 1,000 times that speed.

AI models for the foundations of biology

There is a steadily growing number of industry and academic efforts to build AI models that can derive fundamental biological principles based on protein, RNA, DNA or even cell imaging data, and then use those principles to guide diverse analytical or design tasks. Many of these are described as ‘foundation models’ — a term that broadly describes systems that perform well across a range of different problems through a process of ‘pretraining’ on enormous, unlabeled datasets. This is in contrast to most machine- and deep-learning algorithms in the biology world, which tend to be focused on very specific tasks.

Science for peace: learning from the past

The universal nature of science, with its supposedly neutral language and methods, provides common ground for communication between people - and so can help build peaceful relations between nations. At least, that’s an argument that’s often made, and science historians Roberto Lalli and Jaume Navarro unpick it in an essay for Nature. They explore the many ways that physicists, both individually and collectively, navigated geopolitical tensions throughout the twentieth century, and what scientists more broadly can learn from that when considering responses to, for example, the ongoing war in Ukraine.

The underdogs fighting for the planet

In his new book, The Burning Earth: A History, Sunil Amrith chronicles the fights of the poor and powerless against those seeking to profit from the planet’s natural resources throughout history. A testament to perseverance, Amrith narrates the rebellions of environmentalists over the past 600 years “with flair, in his epic exploration of human innovation and destruction”, writes Josie Glausiusz, as he brings us to the movements still fighting for Earth’s future today.